So I've been working on designing my own ships (see here) as potential alternatives for BFG. But I'd need ordnance as well. I'm planning on making some boarding pods (kinda akin to the Chaos Dreadclaw in scale), torpedos, fighters and bombers. However, I have no clue how big they should be. Does anybody have the dimensions for these models?

Personally I'm not really planning on cloning their stuff. However, that doesn't mean it wouldn't be compatible. Check this thread to see what I'm working on.

I've been thinking about making the ordnance bases shaped like a profile/section of the ship's components from which the originate. So the torpedo base would be shaped like a profile/section of the prow, whilst the fighters base would be a profile/section of the hanger.

I'm not real keen on that idea - as Islacrusez suggests, I don't think your ship sections are that different that they would be easily recognisable in silhouette form. Just make torpedo/attack craft bases a cool shape like maybe triangular

I'd keep them square to maintain compatibility with BFG, where it is used for collisions. You could put a relief on the top of the base, but with actual ordnance models above them it's a little unnecessary. The one thing I can think of is to put little target blips at the base of the stems of individual ordnance, if you're mounting them that way.

What are the dimensions for these bases? Do they all use the same size? As in, is the base for torpedos the same as for fighter craft, etc? I've seen torpedos being mounted on tiny bases (individual torpedos) but also in larger bases (5 in a row or something).

By the FAQ 2010 update, base sizes are 20x20mm, same as the old square epic bases. You are also supposed to mark the size of the wave using dice. Anything smaller than a 10mm d6 is a paint to work with so practically speaking that means the minimum size you can make a base and still be able to easily manipulate 2 dice (waves over 12 are rare for anything other than torpedoes) is 25x25mm.